Blender UV unwrap making too many islands
It isn't that you have non-manifold geometry, it is that the UV seams "cut" the mesh into pieces.

You need to find the separated faces on the mesh and remove the seam from one of the edges so it stays connected.

With both the UV/Image editor and 3D view visible, enable the sync selection option so that the two editors use matching selections. Then Select the UV islands so you can see them on your model and clear some seams to keep them connected to the rest of the mesh.